Search results for: binding kinetics

Authors: Usha Kiran, M. Z. Abdin

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Osmotin is an abundant cationic multifunctional protein discovered in cells of tobacco (Nicotiana tabacum L. var Wisconsin 38) adapted to an environment of low osmotic potential. It provides plants protection from pathogens, hence placed in the PRP family of proteins. The osmotin induced proline accumulation has been reported in plants including transgenic tomato and strawberry conferring tolerance against both biotic and abiotic stresses. The exact mechanism of induction of proline by osmotin is however, not known till date. These observations have led us to hypothesize that osmotin induced proline accumulation could be due to its involvement as transcription factor and/or cell signal pathway modulator in proline biosynthesis. The present investigation was therefore, undertaken to analyze the osmotin protein as transcription factor /cell signalling modulator using bioinformatics tools. The results of available online DNA binding motif search programs revealed that osmotin does not contain DNA-binding motifs. The alignment results of osmotin protein with the protein sequence from DATF showed the homology in the range of 0-20%, suggesting that it might not contain a DNA binding motif. Further to find unique DNA-binding domain, the superimposition of osmotin 3D structure on modeled Arabidopsis transcription factors using Chimera also suggested absence of the same. We, however, found evidence implicating osmotin in cell signaling. With these results, we concluded that osmotin is not a transcription factor but regulating proline biosynthesis and accumulation through cell signaling during abiotic stresses.

Keywords: osmotin, cell signaling modulator, bioinformatic tools, protein

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Authors: Monika Kallubai, Shreya Dubey, Rajagopal Subramanyam

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Our study is all about the biological interactions of synthesized 5β-dihydrocortisol (Dhc) and 5β-dihydrocortisol acetate (DhcA) molecules with carrier protein Human Serum Albumin (HSA). The cytotoxic study was performed on breast cancer cell line (MCF-7) normal human embryonic kidney cell line (HEK293), the IC50 values for MCF-7 cells were 28 and 25 µM, respectively, whereas no toxicity in terms of cell viability was observed with HEK293 cell line. The further experiment proved that Dhc and DhcA induced 35.6% and 37.7% early apoptotic cells and 2.5%, 2.9% late apoptotic cells respectively. Morphological observation of cell death through TUNEL assay revealed that Dhc and DhcA induced apoptosis in MCF-7 cells. The complexes of HSA–Dhc and HSA–DhcA were observed as static quenching, and the binding constants (K) was 4.7±0.03×104 M-1 and 3.9±0.05×104 M-1, and their binding free energies were found to be -6.4 and -6.16 kcal/mol, respectively. The displacement studies confirmed that lidocaine 1.4±0.05×104 M-1 replaced Dhc, and phenylbutazone 1.5±0.05×104 M-1 replaced by DhcA, which explains domain I and domain II are the binding sites for Dhc and DhcA. Further, CD results revealed that the secondary structure of HSA was altered in the presence of Dhc and DhcA. Furthermore, the atomic force microscopy and transmission electron microscopy showed that the dimensions like height and molecular sizes of the HSA–Dhc and HSA–DhcA complex were larger compared to HSA alone. Detailed analysis through molecular dynamics simulations also supported the greater stability of HSA–Dhc and HSA–DhcA complexes, and root-mean-square-fluctuation interpreted the binding site of Dhc as domain IB and domain IIA for DhcA. This information is valuable for the further development of steroid derivatives with improved pharmacological significance as novel anti-cancer drugs.

Keywords: apoptosis, dihydrocortisol, fluorescence quenching, protein conformations

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Authors: D. Bhowmik, Y. Tian, Q. Yin, F. Zhu

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Cyclic GMP-AMP synthase (cGAS), recognises cytoplasmic double-stranded DNA (dsDNA), indicative of bacterial and viral infections, as well as the leakage of self DNA by cellular dysfunction and stresses, to elicit the host's immune responses. Viruses also have developed numerous strategies to antagonize the cGAS-STING pathway. Kaposi's sarcoma-associated herpesvirus (KSHV) is a human DNA tumor virus that is the causative agent of Kaposi’s sarcoma and several other malignancies. To persist in the host, consequently causing diseases, KSHV must overcome the host innate immune responses, including the cGAS-STING DNA sensing pathway. We already found that ORF52 or KicGAS (KSHV inhibitor of cGAS), an abundant and basic gamma herpesvirus-conserved tegument protein, directly inhibits cGAS enzymatic activity. To better understand the mechanism, we have performed the biochemical and structural characterization of full-length KicGAS and various mutants in regarding binding to DNA. We observed that KicGAS is capable of self-association and identified the critical residues involved in the oligomerization process. We also characterized the DNA-binding of KicGAS and found that KicGAS cooperatively oligomerizes along the length of the double stranded DNA, the highly conserved basic residues at the c-terminal disordered region are crucial for DNA recognition. Deficiency in oligomerization also affects DNA binding. Thus DNA binding by KicGAS sequesters DNA and prevents it from being detected by cGAS, consequently inhibiting cGAS activation. KicGAS homologues also inhibit cGAS efficiently, suggesting inhibition of cGAS is evolutionarily conserved mechanism among gamma herpesvirus. These results highlight the important viral strategy to evade this innate immune sensor.

Keywords: Kaposi's sarcoma-associated herpesvirus, KSHV, cGAS, DNA binding, inhibition

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Authors: E. A. Krasikov

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Dependence of the materials properties on neutron irradiation intensity (flux) is a key problem while usage data of the accelerated materials irradiation in test reactors for forecasting of their capacity for work in realistic (practical) circumstances of operation. Investigations of the reactor pressure vessel steel radiation degradation dependence on fast neutron fluence (embrittlement kinetics) at low flux reveal the instability in the form of the scatter of the experimental data and wave-like sections of embrittlement kinetics appearance. Disclosure of the steel degradation oscillating is a sign of the steel structure cyclic self-recovery transformation as it take place in self-organization processes. This assumption has received support through the discovery of the similar ‘anomalous’ data in scientific publications and by means of own additional experiments. Data obtained stimulate looking-for ways to management of the structural steel radiation stability (for example, by means of nano - structure modification for radiation defects annihilation intensification) for creation of the intelligent self-recovering material. Expected results: - radiation degradation theory and mechanisms development, - more adequate models of the radiation embrittlement elaboration, - surveillance specimen programs improvement, - methods and facility development for usage data of the accelerated materials irradiation for forecasting of their capacity for work in realistic (practical) circumstances of operation, - search of the ways for creating of the radiation stable self-recovery intelligent materials.

Keywords: degradation, radiation, steel, wave-like kinetics

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Authors: Leila Vafajoo, Feria Ghanaat, Alireza Mohmadi Kartalaei, Amin Ghalebi

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Petrochemical industries are playing an important role in producing wastewaters. Nowadays different methods are employed to treat these materials. The goal of the present research was to reduce the COD of a petrochemical wastewater via adsorption technique using a commercial granular activated carbon (GAC) as adsorbent. In the current study, parameters of kinetic models as well as; adsorption isotherms were determined through utilizing the Langmuir and Freundlich isotherms. The key parameters of KL= 0.0009 and qm= 33.33 for the former and nf=0.5 and Kf= 0.000004 for the latter isotherms resulted. Moreover, a correlation coefficient of above 90% for both cases proved logical use of such isotherms. On the other hand, pseudo-first and -second order kinetics equations were implemented. These resulted in coefficients of k1=0.005 and qe=2018 as well as; K2=0.009 and qe=1250; respectively. In addition, obtaining the correlation coefficients of 0.94 and 0.68 for these 1st and 2nd order kinetics; respectively indicated advantageous use of the former model. Furthermore, a significant experimental reduction of the petrochemical wastewater COD revealed that, using GAC for the process undertaken was an efficient mean of treatment. Ultimately, the current investigation paved down the road for predicting the system’s behavior on industrial scale.

Keywords: petrochemical wastewater, adsorption, granular activated carbon, equilibrium isotherm, kinetic model

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Authors: Krishnamoorthy Shanmugaraj, Malaichamy Ilanchelian

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Ascorbic acid is an essential component in the diet of humans, and also is a typical long used pharmaceutical agent. In the present contribution, we have carried out a detailed study on the binding interaction of ascorbic acid (AA) with bovine hemoglobin (BHb) using steady state emission, time resolved fluorescence, UV-Vis absorption, circular dichroism (CD), Fourier transform infra-red (FT-IR) and three dimensional emission (3D) spectral studies. The results from the emission spectral studies unveiled that the quenching of BHb emission by AA is attributed to the formation of a complex in the ground state (static in nature) after correcting for inner filter effect. The binding parameters calculated from corrected emission quenching data revealed that BHb exhibited a significant binding affinity towards AA. Moreover, AA induced tertiary and secondary conformational changes of BHb were monitored by UV-Vis absorption, CD, FT-IR and 3D emission spectral studies. The results presented here will help to further understand the credible mechanism of BHb-AA system which is expected to provide insights into conformational and microenvironmental changes of BHb.

Keywords: ascorbic acid, bovine hemoglobin, circular dichroism, three dimensional emission spectral studies

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Authors: J. A. Gbadeyan, R. A. Kareem

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In this paper, we investigated the effects of unsteady internal heat generation of a two-step exothermic reactive hydromagnetic fluid flow under different chemical kinetics namely: Sensitized, Arrhenius and Bimolecular kinetics through an isothermal wall temperature channel. The resultant modeled nonlinear partial differential equations were simplified and solved using a combined Laplace-Differential Transform Method (LDTM). The solutions obtained were discussed and presented graphically to show the salient features of the fluid flow and heat transfer characteristics.

Keywords: unsteady, reactive, hydromagnetic, couette ow, exothermi creactio

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Authors: Fouzia Perveen, Rumana Qureshi

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The presently studied twelve anticancer drugs are the cytotoxic agents which inhibit the replication of DNA and activity of enzymes involved in DNA replication namely topoisomerase-II, polymerase and helicase and have shown remarkable anticancer activity in clinical trials. In this study, we performed molecular docking studies of twelve antitumor drugs against DNA and DNA enzymes in the presence and absence of ascorbic acid (AA) and developed the quantitative structure-activity relationship (QSAR) model for anticancer activity screening. A number of electronic and steric descriptors were calculated using MOE software package. QSAR was established showing a correlation of binding strength with various physicochemical descriptors. Out of these twelve, eight cytotoxic drugs were tested on Non-Small Cell Lung Cancer cell lines (H-157 and H-1299) in the absence and presence of ascorbic acid and experimental IC50 values were calculated. From the docking studies, binding constants were calculated indicating the strength of drug-DNA and drug-enzyme complex formation and it was correlated to the IC50 values (both experimental and theoretical). These results can offer useful references for directing the molecular design of DNA enzyme inhibitor with improved anticancer activity.

Keywords: ascorbic acid, binding constant, cytotoxic agents, cell culture, DNA, DNA enzymes, molecular docking

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Authors: Nagasamy Venkatesh Dhandapani

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The objective of the present study was to develop sustained release oral matrix tablets of anti epileptic drug levetiracetam. The sustained release matrix tablets of levetiracetam were prepared using hydrophilic matrix hydroxypropyl methylcellulose (HPMC) as a release retarding polymer by wet granulation method. Prior to compression, FTIR studies were performed to understand the compatibility between the drug and excipients. The study revealed that there was no chemical interaction between drug and excipients used in the study. The tablets were characterized by physical and chemical parameters and results were found in acceptable limits. In vitro release study was carried out for the tablets using 0.1 N HCl for 2 hours and in phosphate buffer pH 7.4 for remaining time up to 12 hours. The effect of polymer concentration was studied. Different dissolution models were applied to drug release data in order to evaluate release mechanisms and kinetics. The drug release data fit well to zero order kinetics. Drug release mechanism was found as a complex mixture of diffusion, swelling and erosion.

Keywords: levetiracetam, sustained-release, hydrophilic matrix tablet, HPMC grade K 100 MCR, wet granulation, zero order release kinetics

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Authors: Felix U. Asoiro, Meshack I. Simeon, Chinenye E. Azuka, Harami Solomon, Chukwuemeka J. Ohagwu

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The drying kinetics, specific energy consumed (SEC), effective moisture diffusivity (EMD), flavonoid, phenolic, and vitamin C contents of onion slices dried under convective oven drying (COD) were compared with microwave drying (MD). Drying was performed with onion slice thicknesses of 2, 4, 6, and 8 mm; air drying temperatures of 60, 80, and 100°C for COD, and microwave power of 450 W for MD. A decrease in slice thickness and an increase in drying air temperature led to a drop in the drying time. As thickness increased from 2 – 8 mm, EMD rose from 1.1-4.35 x 10⁻⁸ at 60°C, 1.1-5.6 x 10⁻⁸ at 80°C, and 1.25-6.12 x 10⁻⁸ at 100°C with MD treatments yielding the highest mean value (6.65 x 10⁻⁸ m² s⁻¹) at 8 mm. Maximum SEC for onion slices in COD was 238.27 kWh/kg H₂O (2 mm thickness), and the minimum was 39.4 kWh/kg H₂O (8 mm thickness) whereas maximum during MD was 25.33 kWh/kg H₂O (8 mm thickness) and minimum, 18.7 kWh/kg H₂O (2 mm thickness). MD treatment gave a significant (p 0.05) increase in the flavonoid (39.42 – 64.4%), phenolic (38.0 – 46.84%), and vitamin C (3.7 – 4.23 mg 100 g⁻¹) contents, while COD treatment at 60°C and 100°C had positive effects on only vitamin C and phenolic contents, respectively. In comparison, the Weibull model gave the overall best fit (highest R²=0.999; lowest SSE=0.0002, RSME=0.0123, and χ²= 0.0004) when drying 2 mm onion slices at 100°C.

Keywords: allium cepa, drying kinetics, specific energy consumption, flavonoid, vitamin C, microwave oven drying

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Authors: Imene Atek, Abed M. Affoune, Hubert Girault, Pekka Peljo

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Due to the need for a rigorous mathematical model that can help to estimate kinetic properties for soluble-insoluble systems, through voltammetric experiments, a Nicholson Semi Analytical Approach was used in this work for modeling and prediction of theoretical linear sweep voltammetry responses for reversible, quasi reversible or irreversible electron transfer reactions. The redox system of interest is a one-step metal electrodeposition process. A rigorous analysis of simulated linear scan voltammetric responses following variation of dimensionless factors, the rate constant and charge transfer coefficients in a broad range was studied and presented in the form of the so called kinetic zones diagrams. These kinetic diagrams were divided into three kinetics zones. Interpreting these zones leads to empirical mathematical models which can allow the experimenter to determine electrodeposition reactions kinetics whatever the degree of reversibility. The validity of the obtained results was tested and an excellent experiment–theory agreement has been showed.

Keywords: electrodeposition, kinetics diagrams, modeling, voltammetry

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Authors: Milica Karadzic, Lidija Jevric, Sanja Podunavac-Kuzmanovic, Strahinja Kovacevic, Sinisa Markov, Aleksandar Okljesa, Andrea Nikolic, Marija Sakac, Katarina Penov Gasi

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This study considered the microbiological activity determination and molecular docking study for selected steroid derivatives of biomedical importance. Minimal inhibitory concentration (MIC) was determined for steroid derivatives against Staphylococcus aureus using macrodilution method. Some of the investigated steroid derivatives express bacteriostatic effect against Staphylococcus aureus. Molecular docking approaches are the most widely used techniques for predicting the binding mode of a ligand. Molecular docking study was done for steroid derivatives for androgen receptor negative prostate cancer cell line (PC-3) toward Human Cytochrome P450 CYP17A1. The molecules that had the smallest experimental IC50 values confirmed their ability to dock into active place using suitable molecular docking procedure. The binding disposition of those molecules was thoroughly investigated. Microbiological analysis and molecular docking study were conducted with aim to additionally characterize selected steroid derivatives for future investigation regarding their biological activity and to estimate the binding-affinities of investigated derivatives. This article is based upon work from COST Action (TD1305), supported by COST (European Cooperation and Science and Technology).

Keywords: binding affinity, minimal inhibitory concentration, molecular docking, pc-3 cell line, staphylococcus aureus, steroids

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Authors: Ruqaiya Khalil, Saman Usmani, Zaheer Ul-Haq

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The accurate characterization of ligand binding affinity is indispensable for designing molecules with optimized binding affinity. Computational tools help in many directions to predict quantitative correlations between protein-ligand structure and their binding affinities. Molecular dynamics (MD) simulation is a modern state-of-the-art technique to evaluate the underlying basis of ligand-protein interactions by characterizing dynamic and energetic properties during the event. Autoimmune diseases arise from an abnormal immune response of the body against own tissues. The current regimen for the described condition is limited to immune-modulators having compromised pharmacodynamics and pharmacokinetics profiles. One of the key player mediating immunity and tolerance, thus invoking autoimmunity is Interleukin-2; a cytokine influencing the growth of T cells. Molecular dynamics simulation techniques are applied to seek insight into the inhibitory mechanisms of newly synthesized compounds that manifested immunosuppressant potentials during in silico pipeline. In addition to estimation of free energies associated with ligand binding, MD simulation yielded us a great deal of information about ligand-macromolecule interactions to evaluate the pattern of interactions and the molecular basis of inhibition. The present study is a continuum of our efforts to identify interleukin-2 inhibitors of both natural and synthetic origin. Herein, we report molecular dynamics simulation studies of Interluekin-2 complexed with different antagonists previously reported by our group. The study of protein-ligand dynamics enabled us to gain a better understanding of the contribution of different active site residues in ligand binding. The results of the study will be used as the guide to rationalize the fragment based synthesis of drug-like interleukin-2 inhibitors as immune-modulators.

Keywords: immuno-modulators, MD simulation, protein-ligand interaction, structure-based drug design

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Authors: Ude N. Callistus, Amulu F. Ndidi, Onukwuli D. Okechukwu, Amulu E. Patrick

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Power law approximation was used in this study to evaluate the reaction orders of calcium oxide, CaO catalyzed transesterification of refined cottonseed oil and methanol. The kinetics study was carried out at temperatures of 45, 55 and 65 ^oC. The kinetic parameters such as reaction order 2.02 and rate constant 2.8 hr^-1g^-1cat, obtained at the temperature of 65 ^oC best fitted the kinetic model. The activation energy, Ea obtained was 127.744 KJ/mol. The results indicate that the transesterification reaction of the refined cottonseed oil using calcium oxide catalyst is approximately second order reaction.

Keywords: refined cottonseed oil, transesterification, CaO, heterogeneous catalysts, kinetic model

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Authors: Pixiang Wang, Shaoyang Liu, Yucheng Peng

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Polypropylene (PP) is an essential material of numerous applications in different industrial sectors, including packaging, construction, and automotive. Because the application of homopolypropylene (HPP) is limited by its relatively low impact strength and high embrittlement temperature, various types of impact copolymer PP (ICPP) that incorporate elastomers/rubbers into HPP to increase impact strength have been successfully commercialized. Crystallization kinetics of an isotactic HPP, an ICPP, and their composites were studied in this work understand the composites’ behaviors better. The Avrami-Jeziorny model was used to describe the crystallization process. For most samples, the Avrami exponent, n, was greater than 3, indicating the crystal grew in three dimensions with spherical geometry. However, the n value could drop below 3 when the ICPP content was 80 wt.% or higher and the cooling rate was 7.5°C/min or lower, implying that the crystals could grow in two dimensions and some lamella structures could be formed under those conditions. The nucleation activity increased with the increase of the ICPP content, demonstrating that the rubber phase in the ICPP acted as a nucleation agent and facilitated the nucleation process. The decrease in crystallization rate after the ICPP content exceeded 60 wt.% might be caused by the excessive amount of crystal nuclei induced by the high ICPP content, which caused strong crystal-crystal interactions and limited the crystal growth space. The nucleation activity and the n value showed high correlations to the mechanical and thermal properties of the materials. The quantitative study of the kinetics of crystallization in this work could be a helpful reference for manufacturing ICPP and HPP/ICPP mixtures.

Keywords: polypropylene, crystallization kinetics, Avrami-Jeziorny model, crystallization activation energy, Nucleation activity

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Authors: Shahnaz Ashrafpour, Tahereh Tohidi Moghadam, Bijan Ranjbar

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Identifying the nature of protein-nanoparticle interactions and favored binding sites is an important issue in functional characterization of biomolecules and their physiological responses. Herein, interaction of silver nanoparticles with lysozyme as a model protein has been monitored via fluorescence spectroscopy. Formation of complex between the biomolecule and silver nanoparticles (AgNPs) induced a steady state reduction in the fluorescence intensity of protein at different concentrations of nanoparticles. Tryptophan fluorescence quenching spectra suggested that silver nanoparticles act as a foreign quencher, approaching the protein via this residue. Analysis of the Stern-Volmer plot showed quenching constant of 3.73 µM−1. Moreover, a single binding site in lysozyme is suggested to play role during interaction with AgNPs, having low affinity of binding compared to gold nanoparticles. Unfolding studies of lysozyme showed that complex of lysozyme-AgNPs has not undergone structural perturbations compared to the bare protein. Results of this effort will pave the way for utilization of sensitive spectroscopic techniques for rational design of nanobiomaterials in biomedical applications.

Keywords: nanocarrier, nanoparticles, surface plasmon resonance, quenching fluorescence

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Authors: Chongsutthamani Sitthiwet, Praphatsorn Plerdsranoy, Palmarin Dansirima, Priew Eiamlamai, Oliver Utke, Rapee Utke

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Hydrogen storage tank containing compacted LiNH2-LiH is developed by doping with TiF₄ and multi-walled nanotubes (MWCNTs) to study kinetic properties. Transition metal-based catalyst (TiF₄) provides the catalytic effect on hydrogen dissociation/recombination, while MWCNTs benefit thermal conductivity and hydrogen permeability during de/rehydrogenation process. The Enhancement of dehydrogenation kinetics is observed from the single-step reaction at a narrower and lower temperature range of 150-350 ºC (100 ºC lower than the compacted LiNH₂-LiH without additives) as well as long plateau temperature and constant hydrogen flow rate (50 SCCM) up to 30 min during desorption. Besides, Hydrogen contents de/absorbed during 5-6 cycles increase from 1.90-2.40 to 3.10-4.70 wt. % H₂ (from 29 to up to 80 % of theoretical capacity). In the process, Li₅TiN₃ is detected upon cycling probably absorbs NH₃ to form Li₅TiN₃(NH₃)x, which is favoring hydrogen sorption properties of the LiNH₂-LiH system. Importantly, the homogeneous reaction mechanisms and performances are found at all positions inside the tank of compacted LiNH₂-LiH doped with TiF₄ and MWCNTs.

Keywords: carbon, hydride, kinetics, dehydrogenation

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Authors: Abdelmahmod Saad

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In this study two amino acids were chosen (DL.alanine,DL.serine) to determine their effect on dissociation of S2O8-2 ino. As the reaction was very slow, Ag+ ino was used as a catalyst. The kinetics measurement showed that the reactions in both cases were found in the first order with respect to S2O8-2, half order with respect to Ag+ and zero order with respect to substrates. Mechanisms were proposed for these reactions according to the determined orders. The energy of activation (AE) was determined for each reaction, and was found to by 30.50 k JmoI-1 in case of DL. Serine and 24.40 k JmoI-1 in case of DL.alanine.

Keywords: mechanism, oxidation, amino acids, peroxodisulphate

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Authors: Ahmed A. Abdel-Khalek, Reham A. Mohamed

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The kinetics of oxidation of the cobalt (II) complexes, [CoII(ADA)(Gly)(H2O)2]-, (ADA = N-(2-acetamido) iminodi-acetic acid and (Gly = Glycine) by periodate in aqueous acetate medium to cobalt (III) have been studied spectrophotometrically at 530 nm over the 30–50°C and a variety pH 4.57-5.25 range and I = 0.50 mol dm-3 under pseudo first order condition by taking large excess of oxidant [IO4-] and it obeys the following rate law: Rate=[CoII(ADA)(Gly)(H2O)2]-[H5IO6]{k4K6+(k5K7K5/[H+])}. Also, the kinetics of oxidation of the cobalt(II) complexes, [CoII(ADA)(Val)(H2O)2]- (ADA = N-(2-acetamido) iminodi-acetic acid and (Val = valine) by periodate in aqueous medium to cobalt (III) have been studied spectrophotometrically at 580 nm over the 30–50°C and a variety pH 4.3-5.12 range and I = 0.50 mol dm-3 under pseudo first order condition by taking large excess of oxidant [IO4-] and it obeys the following rate law: Rate=[CoII(ADA)(Val)(H2O)2]-[H5IO6]{k4K6+(k5K7K5/[H+])}

Keywords: periodate, oxidation, cobalt (II), glycine, valine acid, n-(2-acetamido imino-diacetato)

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Authors: Laila H. Abdel-Rahman, Mohamed Shaker S. Adam, Ahmed M. Abu-Dief, Hanan El-Sayed Ahmed

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In this investigation, Cu(II), Pd(II) and Ag(I) complexes with the tetra-dentate DSPH Schiff base ligand were synthesized. The DSPH Schiff base and its complexes were characterized by using different physicochemical and spectral analysis. The results revealed that the metal ions coordinated with DSPH ligand through azomethine nitrogen and phenolic oxygen. Cu(II), Pd(II) and Ag(I) complexes are present in a 1:1 molar ratio. Pd(II) and Ag(I) complexes have square planar geometries while, Cu(II) has a distorted octahedral (Oh) geometry. All investigated complexes are nonelectrolytes. The investigated compounds were tested against different strains of bacteria and fungi. Both prepared compounds showed good results of inhibition against the selected pathogenic microorganism. Moreover, the interaction of investigated complexes with CT-DNA was studied via various techniques and the binding modes are mainly intercalative and grooving modes. Operating Environment MOE package was used to do docking studies for the investigated complexes to explore the potential binding mode and energy. Furthermore, the growth inhibitory effect of the investigated compounds was examined on some cancer cells lines.

Keywords: tetradentate, antimicrobial, CT-DNA interaction, docking, anticancer

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Authors: Ali M. Elgerbi, Obied A. Alwan, Al-Taher O. Alzwei, Abdurrahim A. Elouzi

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The binding of AFM1 to bacteria in phosphate buffer solution depended on many factors such as: availability of energy, incubation period, species and strain of bacteria. Increase in concentration of sugar showed higher removal of AFM1 and faster than in phosphate buffer alone. With 1.0% glucose lactic acid bacteria and bifidobacteria showed toxin removal ranging from 7.7 to 39.7% whereas with 10.0% glucose the percentage removal was 21.8 to 45.4% at 96 hours of incubation.

Keywords: aflatoxin M1, lactic acid bacteria, bifidobacteria , binding, phosphate buffer

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Authors: Ahmed K. Youssef, Shawkat M. B. Aly

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The interaction between ciprofloxacin and bovine serum albumin (BSA) was investigated by UV-Visible absorption and fluorescence spectroscopy. The influence of Cu²⁺ Ca²⁺, Co²⁺, and Fe³⁺ on the Cip-BSA interaction was investigated. The quenching of the BSA fluorescence emission in presence of ciprofloxacin as well as the influence of metal ions on the interaction was analyzed using the Stern-Volmer equation. The Stern-Volmer quenching constant, Kₛᵥ was calculated in presence and absence of the metal ions at the physiological pH of 7.4 using phosphate buffer. The experimental results showed that interaction mainly static in nature and quenching rate constant is decreased in presence of the studied metal ions with exception of Cu²⁺ ions. The decrease observed in the Kₛᵥ values in presence of Co²⁺, Ca²⁺, and Fe³⁺ can be understood on basis of competition between these metal and Cip when both of them existed in the BSA solution. Cu²⁺ induces interaction between Cip and BSA at faster quenching rates as inferred from the observed increase in the Kₛᵥ value. This allowed us to propose that copper (II) ions are directly involved in the process of Cip binding to BSA. The binding constant for Cip on BSA was determined and the metal ions effect on it was examined as well and their values were in line with the Kₛᵥ values.

Keywords: bovine serum albumin, ciprofloxacin, fluorescence, metal ions effect

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Authors: Mustafa Sertçelik, Turan Çalban, Hacali Necefoğlu, Sabri Çolak

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In this study, Chevreul’s salt solubility and its dissolution kinetics in ammonium chloride solutions were investigated. Chevreul’s salt that we used in the studies was obtained by using the optimum conditions (ammonium sulphide concentration; 0,4 M, copper sulphate concentration; 0,25 M, temperature; 60°C, stirring speed; 600 rev/min, pH; 4 and reaction time; 15 mins) determined by T. Çalban et al. Chevreul’s salt solubility in ammonium chloride solutions and the kinetics of dissolution were investigated. The selected parameters that affect solubility were reaction temperature, concentration of ammonium chloride, stirring speed, and solid/liquid ratio. Correlation of experimental results had been achieved using linear regression implemented in the statistical package program statistica. The effect of parameters on Chevreul’s salt solubility was examined and integrated rate expression of dissolution rate was found using kinetic models in solid-liquid heterogeneous reactions. The results revealed that the dissolution rate of Chevreul’s salt was decreasing while temperature, concentration of ammonium chloride and stirring speed were increasing. On the other hand, dissolution rate was found to be decreasing with the increase of solid/liquid ratio. Based on result of the applications of the obtained experimental results to the kinetic models, we can deduce that Chevreul’s salt dissolution rate is controlled by diffusion through the ash (or product layer). Activation energy of the reaction of dissolution was found as 74.83 kJ/mol. The integrated rate expression along with the effects of parameters on Chevreul's salt solubility was found to be as follows: 1-3(1-X)2/3+2(1-X)= [2,96.1013.(CA)3,08 .(S/L)-038.(W)1,23 e-9001,2/T].t

Keywords: Chevreul's salt, copper, ammonium chloride, ammonium sulphide, dissolution kinetics

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Authors: Benarous Khedidja, Yousfi Mohamed

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Infections caused by Candida species manifest in a number of diseases, including candidemia, vulvovaginal candidiasis, endocarditis, and peritonitis. These Candida species have been reported to have lipolytic activity by secretion of lipolytic enzymes such as esterases, lipases and phospholipases. These Extracellular hydrolytic enzymes seem to play an important role in Candida overgrowth. Candidiasis is commonly treated with antimycotics such as clotrimazole and nystatin, which bind to a major component of the fungal cell membrane (ergosterol). This binding forms pores in the membrane that lead to death of the fungus. Due to their secondary effects, scientists have thought of another treatment basing on lipase inhibition but we haven’t found any lipase inhibitors used as candidiasis treatment. In this work, we are interested to lipases inhibitors such as alkaloids as another candidiasis treatment. In the first part, we have proceeded to optimize the alkaloid structures and protein 3D structure using Hyperchem software. Secondly, we have docked inhibitors using Genetic algorithm with GOLD software. The results have shown ten possibilities of binding inhibitor to Candida rugosa lipase (CRL) but only one possibility has been accepted depending on the weakest binding energy.

Keywords: marrubiin, candida rugosa lipase, docking, gold

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Authors: Navpreet Kaur, Himkusha Thakur, Nirmal Prabhakar

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The most controversial issue in crop production is the use of Organophosphate insecticides. This is evident in many reports that Organophosphate (OP) insecticides, among the broad range of pesticides are mainly involved in acute and chronic poisoning cases. OPs detection is of crucial importance for health protection, food and environmental safety. In our study, a nanocomposite of poly (3,4 ethylenedioxythiophene) (PEDOT) and multi-walled carbon nanotubes (MWCNTs) has been deposited electrochemically onto the surface of fluorine doped tin oxide sheets (FTO) for the analysis of malathion OP. The -COOH functionalization of MWCNTs has been done for the covalent binding with amino groups of AChE enzyme. The use of PEDOT-MWCNT films exhibited an excellent conductivity, enables fast transfer kinetics and provided a favourable biocompatible microenvironment for AChE, for the significant malathion OP detection. The prepared biosensors were characterized by Fourier transform infrared spectrometry (FTIR), Field emission-scanning electron microscopy (FE-SEM) and electrochemical studies. Various optimization studies were done for different parameters including pH (7.5), AChE concentration (50 mU), substrate concentration (0.3 mM) and inhibition time (10 min). Substrate kinetics has been performed and studied for the determination of Michaelis Menten constant. The detection limit for malathion OP was calculated to be 1 fM within the linear range 1 fM to 1 µM. The activity of inhibited AChE enzyme was restored to 98% of its original value by 2-pyridine aldoxime methiodide (2-PAM) (5 mM) treatment for 11 min. The oxime 2-PAM is able to remove malathion from the active site of AChE by means of trans-esterification reaction. The storage stability and reusability of the prepared biosensor is observed to be 30 days and seven times, respectively. The application of the developed biosensor has also been evaluated for spiked lettuce sample. Recoveries of malathion from the spiked lettuce sample ranged between 96-98%. The low detection limit obtained by the developed biosensor made them reliable, sensitive and a low cost process.

Keywords: PEDOT-MWCNT, malathion, organophosphates, acetylcholinesterase, biosensor, oxime (2-PAM)

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Authors: Nigar Kantarci Carsibasi

Abstract:

Coarse-grained elastic network models, namely Gaussian network model (GNM) and Anisotropic network model (ANM), are utilized in order to investigate the fluctuation dynamics of Murine Double Minute 2 (MDM2), which is the native inhibitor of p53. Conformational dynamics of MDM2 are elucidated in unbound, p53 bound, and non-peptide small molecule inhibitor bound forms. With this, it is aimed to gain insights about the alterations brought to global dynamics of MDM2 by native peptide inhibitor p53, and two small molecule inhibitors (HDM201 and NVP-CGM097) that are undergoing clinical stages in cancer studies. MDM2 undergoes significant conformational changes upon inhibitor binding, carrying pieces of evidence of induced-fit mechanism. Small molecule inhibitors examined in this work exhibit similar fluctuation dynamics and characteristic mode shapes with p53 when complexed with MDM2, which would shed light on the design of novel small molecule inhibitors for cancer therapy. The results showed that residues Phe 19, Trp 23, Leu 26 reside in the minima of slowest modes of p53, pointing to the accepted three-finger binding model. Pro 27 displays the most significant hinge present in p53 and comes out to be another functionally important residue. Three distinct regions are identified in MDM2, for which significant conformational changes are observed upon binding. Regions I (residues 50-77) and III (residues 90-105) correspond to the binding interface of MDM2, including (α2, L2, and α4), which are stabilized during complex formation. Region II (residues 77-90) exhibits a large amplitude motion, being highly flexible, both in the absence and presence of p53 or other inhibitors. MDM2 exhibits a scattered profile in the fastest modes of motion, while binding of p53 and inhibitors puts restraints on MDM2 domains, clearly distinguishing the kinetically hot regions. Mode shape analysis revealed that the α4 domain controls the size of the cleft by keeping the cleft narrow in unbound MDM2; and open in the bound states for proper penetration and binding of p53 and inhibitors, which points to the induced-fit mechanism of p53 binding. P53 interacts with α2 and α4 in a synchronized manner. Collective modes are shifted upon inhibitor binding, i.e., second mode characteristic motion in MDM2-p53 complex is observed in the first mode of apo MDM2; however, apo and bound MDM2 exhibits similar features in the softest modes pointing to pre-existing modes facilitating the ligand binding. Although much higher amplitude motions are attained in the presence of non-peptide small molecule inhibitor molecules as compared to p53, they demonstrate close similarity. Hence, NVP-CGM097 and HDM201 succeed in mimicking the p53 behavior well. Elucidating how drug candidates alter the MDM2 global and conformational dynamics would shed light on the rational design of novel anticancer drugs.

Keywords: cancer, drug design, elastic network model, MDM2

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Authors: Osama K. Abou-Zied, Saba A. Sulaiman

Abstract:

We studied the spectroscopy of 25-nm diameter gold nanoparticles (AuNPs), coated with human serum albumin (HSA) as a model drug carrier. The morphology and coating of the AuNPs were examined using transmission electron microscopy and dynamic light scattering. Resonance energy transfer from the sole tryptophan of HSA (Trp214) to the AuNPs was observed in which the fluorescence quenching of Trp214 is dominated by a static mechanism. Using fluorescein (FL) to probe the warfarin drug-binding site in HSA revealed the unchanged nature of the binding cavity on the surface of the AuNPs, indicating the stability of the protein structure on the metal surface. The transient absorption results of the surface plasmonic resonance (SPR) band of the AuNPs show three ultrafast dynamics that are involved in the relaxation process after excitation at 460 nm. The three decay components were assigned to the electron-electron (~ 400 fs), electron-phonon (~ 2.0 ps) and phonon-phonon (200–250 ps) interactions. These dynamics were not changed upon coating the AuNPs with HSA which indicates the chemical and physical stability of the AuNPs upon bioconjugation. Binding of FL in HSA did not have any measurable effect on the bleach recovery dynamics of the SPR band, although both FL and AuNPs were excited at 460 nm. The current study is important for a better understanding of the physical and dynamical properties of protein-coated metal nanoparticles which are expected to help in optimizing their properties for critical applications in nanomedicine.

Keywords: gold nanoparticles, human serum albumin, fluorescein, femtosecond transient absorption

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Authors: Ratchaneewan Maneemaroj, Paveena Noisuwan, Chonlada Lakhonphon

Abstract:

The smoking is one of the major risk factors in Non-Communicable Disease. Free radicals from cigarette smoke can cause oxidative stress. The oxidative insults can lead to red blood cell (RBC) senescence and are involved in the clearance of red blood cells. The objective of the present study is to assess the association between smoke, oxidative stress evaluated with serum Malondialdehyde (MDA) level and phosphatidylserine (PS) externalization (biomarker of RBC senescence) evaluated with annexin V binding. A total of sixty-four male volunteers aged 25-60 years old were recruited in this study. MDA was measured by colorimetric method. Annexin V binding was detected by flow cytometry. Our results show that there was a significant increase in MDA levels in cigarette smokers as compared to non-smokers (p < 0.001). However, there was no significant different between annexin V binding (% gate) in cigarette smokers and non-smokers (p = 0.978). These results provide evidence of free radical from smoking is associated with oxidative damage to erythrocytes. However, our results suggest that PS externalization is unlikely to have a role in RBC senescence pathway of stressed erythrocytes from cigarette smoke. The other biomarker of RBC senescence should be determined on cigarette smoker erythrocytes.

Keywords: malondialdehyde, phosphatidylserine, RBC senescence, annexin V

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Authors: Bercem Kiran-Yildirim, Volker Gaukel

Abstract:

Ice recrystallization (IR) which occurs especially during frozen storage is an undesired process due to the possible influence on the quality of products. As a result of recrystallization, the total volume of ice remains constant, but the size, number, and shape of ice crystals change. For instance, as indicated in the literature, the size of ice crystals in ice cream increases due to recrystallization. This results in texture deterioration. Therefore, the inhibition of ice recrystallization is of great importance, not only for food industry but also for several other areas where sensitive products are stored frozen, like pharmaceutical products or organs and blood in medicine. Ice-binding proteins (IBPs) have the unique ability to inhibit ice growth and in consequence inhibit recrystallization. This effect is based on their ice binding affinity. In the presence of IBP in a solution, ice crystal growth is inhibited during temperature decrease until a certain temperature is reached. The melting during temperature increase is not influenced. The gap between melting and freezing points is known as thermal hysteresis (TH). In literature, the TH activity is usually investigated under laboratory conditions in IBP buffer solutions. In product applications (e.g., food) there are many other solutes present which may influence the TH activity. In this study, a subset of IBPs, so-called antifreeze proteins (AFPs), is used for the investigation of the influence of sucrose solution concentration on the TH activity. For the investigation, a polarization microscope (Nikon Eclipse LV100ND) equipped with a digital camera (Nikon DS-Ri1) and a cold stage (Linkam LTS420) was used. In a first step, the equipment was established and validated concerning the accuracy of TH measurements based on literature data.

Keywords: ice binding proteins, ice crystals, sucrose solution, thermal hysteresis

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Authors: Phillip Kearney, Constantina Lekakou, Stephen Belcher, Alessandro Sordon

Abstract:

The focus in the automotive industry is to reduce human operator and machine interaction, so manufacturing becomes more automated and safer. The aim is to lower part cost and construction time as well as defects in the parts, sometimes occurring due to the physical limitations of human operators. A move to automate the layup of reinforcement material in composites manufacturing has resulted in the use of tapes that are placed in position by a robotic deposition head, also described as Automated Fibre Placement (AFP). The process of AFP is limited with respect to the finite amount of material that can be loaded into the machine at any one time. Joining two batches of tape material together involves a splice to secure the ends of the finishing tape to the starting edge of the new tape. The splicing method of choice for the majority of prepreg applications is a hand stich method, and as the name suggests requires human input to achieve. This investigation explores three methods for automated splicing, namely, adhesive, binding and stitching. The adhesive technique uses an additional adhesive placed on the tape ends to be joined. Binding uses the binding agent that is already impregnated onto the tape through the application of heat. The stitching method is used as a baseline to compare the new splicing methods to the traditional technique currently in use. As the methods will be used within a High Speed Automated Fibre Placement (HSAFP) process, this meant the parameters of the splices have to meet certain specifications: (a) the splice must be able to endure a load of 50 N in tension applied at a rate of 1 mm/s; (b) the splice must be created in less than 6 seconds, dictated by the capacity of the tape accumulator within the system. The samples for experimentation were manufactured with controlled overlaps, alignment and splicing parameters, these were then tested in tension using a tensile testing machine. Initial analysis explored the use of the impregnated binding agent present on the tape, as in the binding splicing technique. It analysed the effect of temperature and overlap on the strength of the splice. It was found that the optimum splicing temperature was at the higher end of the activation range of the binding agent, 100 °C. The optimum overlap was found to be 25 mm; it was found that there was no improvement in bond strength from 25 mm to 30 mm overlap. The final analysis compared the different splicing methods to the baseline of a stitched bond. It was found that the addition of an adhesive was the best splicing method, achieving a maximum load of over 500 N compared to the 26 N load achieved by a stitching splice and 94 N by the binding method.

Keywords: analysis, automated fibre placement, high speed, splicing

Procedia PDF Downloads 133